I have 4 Gb, but I tried with a more poweful machine in the hospital and I got a similar error. I actually think there is a problem of alignment because the 3 T1s are quiet different from each other: they come from a patient affected by MS with a big lesion in the left frontal lobe. This lesion withdraws drastically in the last T1 as you can see from the two attachments. Moreover, I got a problem in the recon-all, given that freesurfer was not able to reconstruct properly the pial and white surfaces (the gray matter is spared in the patient, however it is not included in the lh.pial surf). Do you think there is a way to edit the brainmask for such a big lesion? Would this solve the problems with the recon-all base?
Thank you!
----Messaggio originale----
Da: theniels@gmail.com
Data: 15-dic-2015 9.31
A: "Freesurfer support list"freesurfer@nmr.mgh.harvard.edu
Ogg: Re: [Freesurfer] recon-all base error
Hi - how much memory do you have on your machine?
On Mon, Dec 14, 2015 at 10:54 AM, salvatoreandrea.92@libero.it salvatoreandrea.92@libero.it wrote: Hi Freesurfer experts!
I tried to run recon-all base for a longitudinal analysis on my data. But I get the following error:
Excessive topologic defect encountered: could not allocate 221309241 edges for retessellation Cannot allocate memory Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/LinuxI tried with a more powerful pc but I encountered the same problem.
Following further information:
SUBJECT template_base DATE ven 11 dic 2015, 08.17.47, CET USER salvatore HOST salvatore-HP-630-Notebook-PC PROCESSOR x86_64 OS Linux Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /home/salvatore/freesurfer/bin/recon-all PWD /home/salvatore/freesurfer/subjects/template_base/scripts CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 template_base lh
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Hi Salvatore,
can you send - the FS version you are using - the recon-all command you called - the recon-all.log file
thanks, Martin
On 12/15/2015 02:00 PM, salvatoreandrea.92@libero.it wrote:
I have 4 Gb, but I tried with a more poweful machine in the hospital and I got a similar error. I actually think there is a problem of alignment because the 3 T1s are quiet different from each other: they come from a patient affected by MS with a big lesion in the left frontal lobe. This lesion withdraws drastically in the last T1 as you can see from the two attachments. Moreover, I got a problem in the recon-all, given that freesurfer was not able to reconstruct properly the pial and white surfaces (the gray matter is spared in the patient, however it is not included in the lh.pial surf). Do you think there is a way to edit the brainmask for such a big lesion? Would this solve the problems with the recon-all base?
Thank you!
----Messaggio originale---- Da: theniels@gmail.com Data: 15-dic-2015 9.31 A: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] recon-all base error Hi - how much memory do you have on your machine? On Mon, Dec 14, 2015 at 10:54 AM, salvatoreandrea.92@libero.it <mailto:salvatoreandrea.92@libero.it> <salvatoreandrea.92@libero.it <mailto:salvatoreandrea.92@libero.it>> wrote: Hi Freesurfer experts! I tried to run recon-all base for a longitudinal analysis on my data. But I get the following error: /Excessive topologic defect encountered: could not allocate 221309241 edges for retessellation Cannot allocate memory Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux/ I tried with a more powerful pc but I encountered the same problem. Following further information: SUBJECT template_base DATE ven 11 dic 2015, 08.17.47, CET USER salvatore HOST salvatore-HP-630-Notebook-PC PROCESSOR x86_64 OS Linux Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /home/salvatore/freesurfer/bin/recon-all PWD /home/salvatore/freesurfer/subjects/template_base/scripts CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 template_base lh _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Martin Reuter -
salvatoreandrea.92＠libero.it